I like the in-season tournament, but they should have the games concentrated and the groups based on regions.
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Northeast: Knicks/Nets/76ers/Toronto/Boston
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Great Lakes: Bulls/Cavs/Bucks/Pistons/Pacers
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Southeast: Wizards/Hornets/Magic/Hawks/Heat
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South: Mavs/Pelicans/Rockets/Grizzlies/Spurs
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West: Suns/Lakers/Clippers/Warriors/Kings
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Northwest (okay..."other"): Blazers/Jazz/Nuggets/Wolves/Thunder
Maybe a better organization than I have there. It gets tricky with groups of five because of the couple of really dense clusters (would prefer OKC with the texas teams, Minny with Great Lakes)... but that's the basic idea. Would be easier to make them more sensible with 5 groups of 6 but then you'd have to redo the knockout format and I like having eight teams advancing.
I think put the group games all together with one team in each region hosting every year on a rotating basis. Try to make the group stages more of an event and over time you get to build up some regional rivalries. Obviously the downside to this is that you could end up with weaker stronger groups, but honestly who cares? Giving some rando team a punchers chance at winning something is kind of what makes this fun. It solves the big problem of having it kind of hard to keep track of who's competing with whom and what the stakes are for every game.